Custom key store not detected in a plain, unused product pack

Description:
When using custom key stores (not with the default wso2carbon.jks file name) for the secret encryption process (using -Dconfigure option), the Cipher tool overrides the key store configurations set in the <PRODUCT_HOME>/repository/conf/security/secret-conf.properties file using the configurations set in the <PRODUCT_HOME>/repository/conf/carbon.xml at the given time.

Thus, any custom key store location path set in the <PRODUCT_HOME>/repository/conf/security/secret-conf.properties in a fresh pack which has not been used before fails, as the initial application of customized key store configurations set in the <PRODUCT_HOME>/repository/conf/deployment.toml to the <PRODUCT_HOME>/repository/conf/carbon.xml happens during the initial execution of the server startup script for the product.

Current workaround:

• Set the custom key store configurations in the product's main configuration file <PRODUCT_HOME>/repository/conf/deployment.toml
• Add the custom key stores to the <PRODUCT_HOME>/repository/resources/security directory
• Execute the product server startup script
• Set the secrets in the <PRODUCT_HOME>/repository/conf/deployment.toml file
• Encrypt the secrets using the Cipher tool

Used Product and Version:
WSO2 Identity Server version 5.11.0 Release Candidate 1

Start by tracing the Cipher tool's handling of repository/conf/security/secret-conf.properties and repository/conf/carbon.xml when -Dconfigure is used. Compare this with the initial startup processing of repository/conf/deployment.toml and the resources/security directory. Done means a custom key store in a fresh, unused product pack is detected without the listed startup workaround.